Structure of PDB 6wjy Chain B Binding Site BS01

Receptor Information
>6wjy Chain B (length=375) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVE
KLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVP
YCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCS
KGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKA
LQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFA
GGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSL
ESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQ
QGGTDLMNFLKTVRSTTEKSLLKEG
Ligand information
Ligand IDU41
InChIInChI=1S/C21H20ClFN2O2/c1-13(18(26)24-17-7-5-16(23)6-8-17)20-10-21(11-20,12-20)25-19(27)14-3-2-4-15(22)9-14/h2-9,13H,10-12H2,1H3,(H,24,26)(H,25,27)/t13-,20-,21+/m1/s1
InChIKeyORFXTXYARYWSKK-PZVFOTJXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[C@H](C(=O)Nc1ccc(cc1)F)C23CC(C2)(C3)NC(=O)c4cccc(c4)Cl
OpenEye OEToolkits 2.0.7CC(C(=O)Nc1ccc(cc1)F)C23CC(C2)(C3)NC(=O)c4cccc(c4)Cl
CACTVS 3.385C[C@H](C(=O)Nc1ccc(F)cc1)C23CC(C2)(C3)NC(=O)c4cccc(Cl)c4
CACTVS 3.385C[CH](C(=O)Nc1ccc(F)cc1)C23CC(C2)(C3)NC(=O)c4cccc(Cl)c4
ACDLabs 12.01C(=O)(c1cccc(c1)Cl)NC24CC(C2)(C(C(=O)Nc3ccc(cc3)F)C)C4
FormulaC21 H20 Cl F N2 O2
Name3-chloro-N-(3-{(2S)-1-[(4-fluorophenyl)amino]-1-oxopropan-2-yl}bicyclo[1.1.1]pentan-1-yl)benzamide
ChEMBL
DrugBank
ZINC
PDB chain6wjy Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6wjy Discovery of Potent and Orally Available Bicyclo[1.1.1]pentane-Derived Indoleamine-2,3-dioxygenase 1 (IDO1) Inhibitors.
Resolution1.91 Å
Binding residue
(original residue number in PDB)		Y126 C129 V130 F163 S167 F214 G262 S263 A264 V269 L342
Binding residue
(residue number reindexed from 1)		Y116 C119 V120 F153 S157 F204 G252 S253 A254 V259 L332
Annotation score1
Binding affinityMOAD: ic50=3.1nM
BindingDB: IC50=3.1nM
Enzymatic activity
Enzyme Commision number 1.13.11.52: indoleamine 2,3-dioxygenase.
Gene Ontology
Molecular Function
GO:0004833 tryptophan 2,3-dioxygenase activity
GO:0009055 electron transfer activity
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0020037 heme binding
GO:0033754 indoleamine 2,3-dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0002376 immune system process
GO:0002666 positive regulation of T cell tolerance induction
GO:0002678 positive regulation of chronic inflammatory response
GO:0002830 positive regulation of type 2 immune response
GO:0006569 tryptophan catabolic process
GO:0006954 inflammatory response
GO:0007565 female pregnancy
GO:0019441 tryptophan catabolic process to kynurenine
GO:0019805 quinolinate biosynthetic process
GO:0032496 response to lipopolysaccharide
GO:0032693 negative regulation of interleukin-10 production
GO:0032735 positive regulation of interleukin-12 production
GO:0033555 multicellular organismal response to stress
GO:0034276 kynurenic acid biosynthetic process
GO:0034354 'de novo' NAD biosynthetic process from tryptophan
GO:0036269 swimming behavior
GO:0042098 T cell proliferation
GO:0042130 negative regulation of T cell proliferation
GO:0043065 positive regulation of apoptotic process
GO:0046006 regulation of activated T cell proliferation
GO:0070233 negative regulation of T cell apoptotic process
GO:0070234 positive regulation of T cell apoptotic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030485 smooth muscle contractile fiber
GO:0032421 stereocilium bundle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6wjy, PDBe:6wjy, PDBj:6wjy
PDBsum6wjy
PubMed32832022
UniProtP14902|I23O1_HUMAN Indoleamine 2,3-dioxygenase 1 (Gene Name=IDO1)

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